def clean_consensus_outputs( dir_path, output_file ):
for filename in os.listdir( dir_path ):
file_path = os.path.join( dir_path, filename )
if file_path.endswith('_input.fa'):
os.remove( file_path )
elif file_path.endswith('_input.fa.aln'):
os.remove( file_path )
elif file_path.endswith('_input.fa.aln_unsorted'):
os.remove( file_path )
write_dummy_file( output_file )
def clean_consensus_outputs(dir_path, output_file):
for filename in os.listdir(dir_path):
file_path = os.path.join(dir_path, filename)
if file_path.endswith('_input.fa'):
os.remove(file_path)
elif file_path.endswith('_input.fa.aln'):
os.remove(file_path)
elif file_path.endswith('_input.fa.aln_unsorted'):
os.remove(file_path)
write_dummy_file(output_file)
def cleanup_uchime_output(self, screenedFile):
outputFile = self.process_setup(screenedFile,
'UchimeCleanup',
suffix='uchime.cleanup')
uchimePath = os.getcwd()
for filename in os.listdir(uchimePath):
if filename.endswith('_formatted'):
file_path = os.path.join(uchimePath, filename)
os.remove(file_path)
write_dummy_file(outputFile)
self.process_cleanup(output_file=outputFile)
return outputFile
def cleanup_uchime_output( self, screenedFile ):
outputFile = self.process_setup( screenedFile,
'UchimeCleanup',
suffix='uchime.cleanup' )
uchimePath = os.getcwd()
for filename in os.listdir( uchimePath ):
if filename.endswith('_formatted'):
file_path = os.path.join( uchimePath, filename )
os.remove( file_path )
write_dummy_file( outputFile )
self.process_cleanup(output_file=outputFile)
return outputFile